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biopandas version: 0.2.1

PandasPdb

PandasPdb()

Object for working with Protein Databank structure files.

Attributes

  • df : dict

    Dictionary storing pandas DataFrames for PDB record sections. The dictionary keys are {'ATOM', 'HETATM', 'ANISOU', 'OTHERS'} where 'OTHERS' contains all entries that are not parsed as 'ATOM', 'HETATM', or 'ANISOU'

  • pdb_text : str

    PDB file contents in raw text format

  • header : str

    PDB file description

  • code : str

    PDB code

Methods

amino3to1(record='ATOM', residue_col='residue_name', fillna='?')

Creates 1-letter amino acid codes from DataFrame

Non-canonical amino-acids are converted as follows:
ASH (protonated ASP) => D
CYX (disulfide-bonded CYS) => C
GLH (protonated GLU) => E
HID/HIE/HIP (different protonation states of HIS) = H
HYP (hydroxyproline) => P
MSE (selenomethionine) => M

Parameters

  • record : str (default: 'ATOM')

    Specfies the record DataFrame

  • residue_col : str (default: 'residue_name')

    Column in record DataFrame to look for 3-letter amino acid codes for the conversion

  • fillna : str (default: '?')

    Placeholder string to use for unknown amino acids

Returns

  • pandas.DataFrame : Pandas DataFrame object consisting of two columns,

    'chain_id' and 'residue_name', where the former contains the chain ID of the amino acid and the latter contains the 1-letter amino acid code, respectively.

distance(xyz=(0.0, 0.0, 0.0), record='ATOM')

Computes Euclidean distance between atoms and a 3D point.

Parameters

  • xyz : tuple (0.00, 0.00, 0.00)

    X, Y, and Z coordinate of the reference center for the distance computation

  • record : str (default: 'ATOM')

    Specfies the record DataFrame

Returns

  • pandas.Series : Pandas Series object containing the Euclidean

    distance between the atoms in the record section and xyz.

fetch_pdb(pdb_code)

Fetches PDB file contents from the Protein Databank at rcsb.org.

Parameters

  • pdb_code : str

    A 4-letter PDB code, e.g., "3eiy"

Returns

self

get(s, df=None, invert=False)

Filter PDB DataFrames by properties

Parameters

  • s : str in {'main chain', 'hydrogen', 'c-alpha', 'heavy'}

    String to specify which entries to return

  • df : pandas.DataFrame, default: None

    Optional DataFrame to perform the filter operation on. If df=None, filters on self.df['ATOM']

  • invert : bool, default: True

    Inverts the search query. For example if s='hydrogen' and invert=True, all but hydrogen entries are returned

Returns

  • df : pandas.DataFrame

    Returns a DataFrame view on the filtered entries.

impute_element(sections=('ATOM', 'HETATM'), inplace=False)

Impute element_symbol from atom_name section.

Parameters

  • sections : iterable (default: ('ATOM', 'HETATM'))

    Coordinate sections for which the element symbols should be imputed.

  • inplace : bool (default: False)

    Performs the operation in-place if True and returns a copy of the PDB DataFrame otherwise.

Returns

DataFrame

read_pdb(path)

Read PDB files (unzipped or gzipped) from local drive

Attributes

  • path : str

    Path to the PDB file in .pdb format or gzipped format (.pdb.gz)

Returns

self

rmsd(df1, df2, s=None, invert=False)

Compute the Root Mean Square Deviation between molecules.

Parameters

  • df1 : pandas.DataFrame

    DataFrame with HETATM, ATOM, and/or ANISOU entries

  • df2 : pandas.DataFrame

    Second DataFrame for RMSD computation against df1. Must have the same number of entries as df1

  • s : {'main chain', 'hydrogen', 'c-alpha', 'heavy', 'carbon'} or None,

    default: None String to specify which entries to consider. If None, considers all atoms for comparison.

  • invert : bool, default: False

    Inverts the string query if true. For example, the setting s='hydrogen', invert=True computes the RMSD based on all but hydrogen atoms.

Returns

  • rmsd : float

    Root Mean Square Deviation between df1 and df2

to_pdb(path, records=None, gz=False, append_newline=True)

Write record DataFrames to a PDB file or gzipped PDB file.

Parameters

  • path : str

    A valid output path for the pdb file

  • records : iterable, default: None

    A list of PDB record sections in {'ATOM', 'HETATM', 'ANISOU', 'OTHERS'} that are to be written. Writes all lines to PDB if records=None

  • gz : bool, default: False

    Writes a gzipped PDB file if True

  • append_newline : bool, default: True

    Appends a new line at the end of the PDB file if True

Properties

df

Acccess dictionary of pandas DataFrames for PDB record sections.